The prevalence and microbiology of concomitant respiratory bacterial infections in patients with SARS-CoV-2 infection are not yet fully understood. In this retrospective study, we assessed respiratory bacterial co-infections in lower respiratory tract samples taken from intensive care unit-hospitalized COVID-19 patients, by comparing the conventional culture approach to an innovative molecular diagnostic technology. A total of 230 lower respiratory tract samples (i.e., bronchial aspirates or bronchoalveolar lavages) were taken from 178 critically ill COVID-19 patients. Each sample was processed by a semi-quantitative culture and by a multiplex PCR panel (FilmArray Pneumonia Plus panel), allowing rapid detection of a wide range of clinically relevant pathogens and a limited number of antimicrobial resistance markers. More than 30% of samples showed a positive bacterial culture, with Pseudomonas aeruginosa , Klebsiella pneumoniae and Staphylococcus aureus the most detected pathogens. FilmArray showed an overall sensitivity and specificity of 89.6% and 98.3%, respectively, with a negative predictive value of 99.7%. The molecular test significantly reduced the turn-around-time (TAT) and increased the rates of microbial detection. Most cases missed by culture were characterized by low bacterial loads (10 4 –10 5 copies/mL). FilmArray missed a list of pathogens not included in the molecular panel, especially Stenotrophomonas maltophilia (8 cases). FilmArray can be useful to detect bacterial pathogens in lower respiratory tract specimens of COVID-19 patients, with a significant decrease of TAT. The test is particularly useful to rule out bacterial co-infections and avoid the inappropriate prescription of antibiotics.

Candida species are the most common cause of opportunistic fungal infections. Rapid identification and novel approaches for the characterization of these fungi are of great interest to improve the diagnosis and the knowledge about their pathogenic properties. This study aimed to characterize clinical isolates of Candida spp. by proteomics (MALDI-TOF MS) and metabolomics (1H-NMR), and to correlate their metabolic profiles with Candida species, source of infection and different virulence associated parameters. In particular, 49 Candida strains from different sources (blood, n = 15; vagina, n = 18; respiratory tract, n = 16), belonging mainly to C. albicans complex (61%), C. glabrata (20%) and C. parapsilosis (12%) species were used. Several extracellular and intracellular metabolites showed significantly different concentrations among isolates recovered from different sources of infection, as well as among different Candida species. These metabolites were mainly related to the glycolysis or gluconeogenesis, tricarboxylic acid cycle, nucleic acid synthesis and amino acid and lipid metabolism. Moreover, we found specific metabolic fingerprints associated with the ability to form biofilm, the antifungal resistance (i.e. caspofungin and fluconazole) and the production of secreted aspartyl proteinase. In conclusion, 1H-NMR-based metabolomics can be useful to deepen Candida spp. virulence and pathogenicity properties.

Objectives The COVID-19 pandemic has intensified interest in how the infection impacts the lung microbiome of critically ill patients and contributes to acute respiratory distress syndrome (ARDS). We aimed to characterize the lower respiratory tract mycobiome of COVID-19 critically ill patients in comparison to COVID-19-negative patients. Methods We performed an Internal transcribed spacer 2 (ITS2) profiling, with the Illumina MiSeq platform, on 26 respiratory specimens from COVID-19 positive patients as well as from 26 patients with non-COVID-19 pneumonia. Results COVID-19+ patients were more likely to be colonized with Candida spp. and ARDS was associated with lung dysbiosis characterised by a shift to Candida species colonisation and a decrease of fungal diversity. We also observed higher bacterial phylogenetic distance among taxa in COVID-19+ colonized patients. In COVID-19+ patients non-colonized with Candida spp , ITS2 amplicon sequencing revealed an increase of Ascomycota unassigned spp. and one Aspergillus spp positive specimen. Then, we found that corticosteroid therapy was frequently associated with positive Galactomannan cell wall component of Aspergillus spp among COVID-19+ patients. Conclusions Our study underpins that ARDS in COVID-19+ patients is associated with lung dysbiosis and that an increased density of Ascomycota unassigned spp. is present in patients not colonized with Candida spp .

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We report for the first time the occurrence of a filamentous fungus, Albifimbria verrucaria, in the blood of a pediatric neuroblastoma patient. The Albifimbria genus comprises common soil-inhabiting and saprophytic fungi and has been isolated as a plant pathogen in Northern and Southern Italy. As a human pathogen, A. verrucaria has been implicated in keratitis and can produce trichothecene toxins, which are weakly cytotoxic for mammalian cell lines. A. verrucaria was isolated from blood during the follow-up of a previous coagulase-negative Staphylococcus catheter-related infection. Lung nodules, compatible with fungal infection, had been observed on a CT scan 6 months earlier; they still persist. Possible routes of transmission were considered to be airborne, catheter related, or transfusion dependent, as the patient had undergone platelet and red blood cell transfusions during rescue chemotherapy. No filamentous fungi were isolated from sputum or CVCs. In conclusion, we describe an unprecedented fungemia caused by A. verrucaria and show how an unexpected pathogen may be acquired from the environment by patients at high risk due to immunosuppression. The route of transmission remains unknown.